The boyfriend of the 13-year-old Bronx girl who allegedly threw her newborn out of a second-floor window had begged her to tell her family she was pregnant, his sister said yesterday.

Instead, the expectant teen wore winter coats to hide her condition and told her 15-year-old boyfriend she was afraid her brothers would kill him if they found out he had gotten her pregnant, the sister said.

“He kept telling her to tell her family,” said the boy’s sister, whose name is being withheld by The Post.

The teenage parents have not been charged in the baby’s death.

“He tried to talk to her brothers, but they threatened him,” the sister added.

The deception ended in tragedy early Friday, when the girl gave birth alone in her bedroom while her mother slept, and threw the baby out the window in panic when he began to cry, cops said.

She then went to school after leaving the infant in the freezing alley where he had landed, the father’s sister said.

The young dad found the baby after school when the girl told him of the birth. Terrified, the boy left the baby in a “Happy Birthday” gift bag outside the Second Prince of Peace Baptist Church on East 183rd Street, a few blocks from the girl’s apartment, cops said.

Passer-by Willie Vasquez discovered the bag with the infant’s body inside, its unbiblical cord still attached, at around 8:20 p.m.

An autopsy revealed that his head was fractured and his leg broken.

Authorities were not certain exactly when the baby died.

The Bronx District Attorney’s Office said yesterday it is still investigating and plans to bring the case before a grand jury as early as today.

The teen mother is being treated in The Bronx Psychiatric Center.

A cousin of the mother, who lives near her apartment in Tremont, said the family did not know she was pregnant.

“She probably hid it. I didn’t even know and I used to see her every day,” said the cousin who gave his name only as Dred.

The sister of the baby’s father said the teen, who lives with his mother in a family shelter in Manhattan, was devastated by the death of his baby.

“He’s really grieving. He’s really bad right now,” she said. “He knew she was going to have the baby, and he kept telling her to tell someone.”

The sister said her family would have willingly taken in the baby.

Other relatives placed a card at a shrine at the church, which read, “We will love you and miss you. From your grandparents, your aunts. Lazarro Jr., [we] love you always. We’ll miss you.”